NOTE - see middle of page for previous weeks' schedules and things to catch up on.
Definitions: 'cubby' = VDS cabinet in back of lab where all of our reagents are; 'pigeon hole' = the shelf for your lab notebook over by the window
This Week
This Week
SPRINGERS
VETERANS
ITEMS FOR THE WEEK:
Enzyme assays with your surrogate enzyme: ProtocolEnzymeTest_Phosphatase_VDS_Fall12_varyEnzyme.xlsx
Start Inhibition assays. ProtocolEnzymeTest_Phosphatase_VDS_Fall12_Inhibition.xlsx
Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)
Finish Virtual Screening
cb306 and CBkinUT
3-Dec Monday 4-Dec Tuesday 5-Dec Wednesday
LAST VDS CLASS
Class Picture!
In class on Wednesday (12/5) - around 75% of the way through class ~ 2:45
VDSers - don't forget to fill out the CIS forms online. We won't do a paper version this semester.
CH 369K (52275) https://utdirect.utexas.edu/ctl/ecis/
6-Dec Thursday
Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
7-Dec Friday
Lab Cleanup
8-Dec Saturday
Final Lab Report Due
Final LAB NOTEBOOK CHECK
9-Dec Sunday
ITEMS FOR THE WEEK:
continue with wet lab work
Start Inhibition assays. Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)
Analyze and post your library screening results to GDocs
3-Dec Monday 4-Dec Tuesday 5-Dec Wednesday
LAST VDS CLASS
Class Picture!
In class on Wednesday (12/5) - around 75% of the way through class ~ 2:45
VDSers - don't forget to fill out the CIS forms online. We won't do a paper version this semester.
CH 369K (52275) https://utdirect.utexas.edu/ctl/ecis/
6-Dec Thursday
Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
7-Dec Friday
Lab Cleanup
8-Dec Saturday
Final Lab Report Due
Final LAB NOTEBOOK CHECK
9-Dec Sunday
Next Week
Next Week
SPRINGERS
VETERANS
ITEMS FOR THE WEEK:
ITEMS FOR THE WEEK:
Dr. B Notes
Enzyme Assay kinetics lab (phosphatase)
Protein Protocols to be completed - also see instructional videos on GDocs
ProtocolProteinExpression_VDS_Fall12.doc
ProtocolProteinPurificationVDS_Fall12.doc ProtocolHomemadeSDSPageGelSolutionsVDS_Fall12.docx - Skip this one (the Mentors will make gels for you)
ProtocolProteinCharacterizationVDS_Fall12.doc
ProtocolFPLC_GelFiltration_VDS_Fall12.docx
ProtocolLabEnzymeTest_Phosphatase_VDS_Fall12.xlsx
Enzyme Assays on target
Inhibition Assays on target
Optional: VINA tutorial BASH or Perl script
ORDER Primers for you target
PRIMER ORDERING SESSION: 1 - 4:30 in WEL 2.114 - Comp Lab
Spreadsheet for ordering primers is at:
Google Docs/VDS/Misc/Primers/PrimerPlateOrderTemplate_GDocs_AugFall_2012
Wikispaces check on each Friday
Your WikiPage should have: been created by now, brief detail of what you have done these last 3 days
PAPER COPY – Print out of TxClass Safety Training - (can put in Safety section of VDS sign-in binder in lab)
submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev)
-- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc
1-Sep Saturday 2-Sep Sunday
Download & print needed protocols from GDocs
-- under /Protocols/Cloning/FirstProtocols
Submit to DNA Sequencing
-- in 2 days retrieve and save results to your GDocs folder
RE Digest
-- save results to your GDocs folder
-- post image commentary to your Wikispace page
Analyze DNA sequence exercise
Virtual Screening Refresher
Finish cloning your gene into pNIC-Bsa4
Transform positive clone with your gene into BL21(De3) cells - begin expression
PyMol Refresher - Due by ??
Science Works assignment due ??
27-Aug Monday
28-Aug Tuesday
29-Aug Wednesday
2 - 3pm - Lab Group Meeting/Journal Club (in ???? classroom)
30-Aug Thursday
31-Aug Friday
PyMol Refresher - due next Wed
Wikispaces check on each Friday
1-Sep Saturday 2-Sep Sunday
Submit to DNA Sequencing
-- in 2 days retrieve and save results to your GDocs folder
RE Digest
-- save results to your GDocs folder
-- post image commentary to your Wikispace page
3-Sep Monday
12 - 4 pm Target Discovery & Primer Design & Primer ordering
Spreadsheet for ordering primers is at:
Google Docs/VDS/Misc/Primers/PrimerPlateOrderTemplate_GDocs_AugFall_2012
4-Sep Tuesday
If your primers have been uploaded:
ProtocolPrimerDilutionVDS_Fall12.docx (use pLIC for or pLIC rev)
-- submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev)
---- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc
Target Discovery
PAPER COPY – Print out of TxClass Safety Training - (can put in Safety section of VDS sign-in binder in lab)
5-Sep Wednesday
2 - 3pm - Lab Group Meeting (in RLM 11.176 classroom)
ProtocolPrimerDilutionVDS_Fall12.docx (use pLIC for or pLIC rev) (~1.5 hrs)
-- submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev)
---- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc
Transformation of pNIC-Bsa4 in Dh5alpha (~2-2.5 hrs)
6-Sep Thursday
Retrieve results on line from DNA Sequencing core website for your results from:
-- "Submit to DNA Sequencing"
- save results to your GDocs folder
RE digest & Agarose Gel - of pGBR22
--- ProtocolRestrictionEnzymeDigestVDS.doc (~4hrs with break)
--- ProtocolNanoDropVDS.doc (~2hrs)
Transformation of pNIC-Bsa4 in Dh5alpha
7-Sep Friday
Springers - Finish up your Target page that you created in Target Discovery Protocol, even if it was not one that was chosen. This will be for a grade.
3:30 - 6:30 Analyze DNA sequence exercise (in WELCH computer lab)
-- save the assignment as WORD doc to your GDocs folder
Wikispaces check on each Friday
Your WikiPage should have
images of all PCR gels (well annotated - i.e. descriptions and what each lane is)
image of RE digest gel (well annotated)
Paste a copy of your DNA sequence from the DNA sequencing core (briefly describe what it is)
8-Sep Saturday 9-Sep Sunday
3-Sep Monday
Help Sessions: PyMol and Virtual Screen Refresher Welch Computer Lab
4-Sep Tuesday
5-Sep Wednesday
2 - 3pm - Lab Group Meeting (in RLM 11.176 classroom)
PyMol Refresher - due today
6-Sep Thursday
7-Sep Friday
New Overlap PCR protocol posted to GDocs that uses new Q5 polymerase from NEB -- courtesy of Kaarthik
---ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall12.docx
You can use either Q5 or KOD polymerase. But we are out of KOD right now!
8-Sep Saturday 9-Sep Sunday
1. RE digest & Agarose Gel - of pGBR22
--- ProtocolRestrictionEnzymeDigestVDS.doc (~4hrs with break)
--- ProtocolNanoDropVDS.doc (~2hrs)
2. Retrieve results on line from DNA Sequencing core website for your results from:
-- "Submit to DNA Sequencing"
- save results to your GDocs folder
PAPER COPY – Print out of TxClass Safety Training - (can put in Safety section of VDS sign-in binder in lab)
3. Grow up pNIC_bsa4 in DH5alpha o/n in 1x160ml - store pellets
4. Midi prep pNIC-Bsa4 (later in week - Th or Fri in groups)
5. Practice PCR #1: ProtocolPCRVDS.xls with TAQ poly
10-SepMonday 11-SepTuesday 12-SepWednesday
2 - 3pm - Lab Group Meeting(in NEW classroom: RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
13-SepThursday 14-SepFriday --FRI Picnic (Mentors & Dr. B) Lab Notebook Check this Friday - leave your notebook in your 'pigeon hole' in lab by 7:00 pm
all protocols (PCR , RE Digest, analyze DNA, submit DNA)
all gel images
Analyze DNA Sequence exercise work
Protocol, Order form and Results from ProtocolDNASequencingFacilityVDS_Fall11.doc
15-SepSaturday 16-SepSunday - Wikispaces check on each Sunday night by 9:00 pm
clone your gene!
New Overlap PCR protocol posted to GDocs that uses new Q5 polymerase from NEB -- courtesy of Kaarthik
---ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall12.docx
Virtual Screen Refresher - due next week (Friday Sept 22nd)
10-SepMonday 11-SepTuesday 12-SepWednesday
2 - 3pm - Lab Group Meeting(in NEW classroom: RLM 10.176)
--------- includes JOURNAL CLUB*
13-SepThursday 14-SepFriday --5-7pm FRI Picnic (Mentors & Dr. B)
Lab Notebook Check this Friday - leave your notebook in your 'pigeon hole' in lab by 7:00 pm
15-SepSaturday 16-SepSunday - Wikispaces check on each Sunday night by 9:00 pm
ITEMS FOR THE WEEK: Should have already completed: RE digest, Nanodrop, Submit to DNA, Analyze DNA, Transformation, etc.
(NOTE: be sure to post your Nanodrop concentrations of pNIC-Bsa4 from MidiPrep on the Google Docs spreadsheet
- in /Misc/PlasmidConcentrations. ONLY a few of you have uploaded yours.
Midi prep pNIC-Bsa4
Practice PCR #1: ProtocolPCRVDS.xlswith TAQ poly
this PCR must work correctly before you can proceed
Practice PCR #2: ProtocolPCR_pLICsequencing.xls on pNIC-Bsa4 with Taq poly using pLicFor and pLicRev
17-SepMonday 18-SepTuesday 19-SepWednesday -
2 - 3pm - Lab Group Meeting(in NEW classroom: RLM 10.176)
20-SepThursday 21-SepFriday ? FRI Picnic (Mentors & Dr. B)?? 22-SepSaturday 23-SepSunday - Wikispaces check on each Sunday night by 9:00 pm
ITEMS FOR THE WEEK: Continue cloning
Virtual Screen Refresher - due (Friday Sept 22nd)
17-SepMonday 18-SepTuesday 19-SepWednesday
2 - 3pm - Lab Group Meeting(in NEW classroom: RLM 10.176)
20-SepThursday 21-SepFriday ? FRI Picnic (Mentors & Dr. B)?? 22-SepSaturday 23-SepSunday - Wikispaces check on each Sunday night by 9:00 pm
(NOTE: be sure to post your Nanodrop concentrations of pNIC-Bsa4 from MidiPrep on the Google Docs spreadsheet
- in /Misc/PlasmidConcentrations. ONLY a few of you have uploaded yours.
Practice PCR #2: ProtocolPCR_pLICsequencing.xls on pNIC-Bsa4 with Taq poly using pLicFor and pLicRev
this is a priority - Dr. B has to check it before we can order them
- post final primers to Wikispaces page
ProtocolPCR_PrimerOverlapVDS_fall12.docx
- 1st step is to Make Oligo Mix (takes an hour or two)
24-SepMonday 25-SepTuesday 26-SepWednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
27-SepThursday 28-SepFriday
29-SepSaturday
PyMol refresher due date changed to this Saturday Sept 29th
30-SepSunday - Wikispaces check on each Sunday night by 9:00 pm
-- PyMol refresher due date changed again to this Sunday Sept 30th - i would rather you focus on your
---- ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall12.doc
24-SepMonday 25-SepTuesday 26-SepWednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
27-SepThursday 28-SepFriday 29-SepSaturday 30-SepSunday - Wikispaces check on each Sunday night by 9:00 pm
ProtocolPCR_PrimerOverlapVDS_Fall12.docx
-- 1st step: Make Oligo Mix
-- 2nd step: Primary PCR
-- 3rd step: Secondary PCR - need your custom 'tail' primers for this
-- RE digest of pNIC-Bsa4 (save for yourself and use for cloning) - NOTE: different than last RE digest
------ takes 4 hrs (3 hours of incubation in 37degC water bath - you can leave during this time)
-- Clone your gene into accepting vector
---------ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc
4-Oct Thursday 5-Oct Friday 6-Oct Saturday 7-Oct Sunday - Wikispaces check on each Sunday night by 9:00 pm
(NOTE: be sure to post your Nanodrop concentrations of pNIC-Bsa4 from MidiPrep on the Google Docs spreadsheet
- in /Misc/PlasmidConcentrations. ONLY a few of you have uploaded yours.
4-Oct Thursday 5-Oct Friday 6-Oct Saturday 7-Oct Sunday - Wikispaces check on each Sunday night by 9:00 pm
ProtocolPCR_PrimerOverlapVDS_Fall12.docx
-- 2nd step: Primary PCR
-- 3rd step: Secondary PCR - need your custom 'tail' primers for this
-- RE digest of pNIC-Bsa4 (save for yourself and use for cloning) - NOTE: different than last RE digest
------ takes 4 hrs (3 hours of incubation in 37degC water bath - you can leave during this time)
-- Clone your gene into accepting vector
ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc
8-Oct Monday 9-Oct Tuesday 10-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
11-Oct Thursday 12-Oct Friday 13-Oct Saturday 14-Oct Sunday - Wikispaces check on each Sunday night by 9:00 pm
Should be finishing cloning
Virtual Screening Protocols are posted (these are for your real target - not practice)
in GDOCS /Protocols/VirtualScreeningProtocols/
ProtocolHomologyModelVDS_v3.doc
ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
Protocol_ICM_VDSv1_3.docx
8-Oct Monday 9-Oct Tuesday 10-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
11-Oct Thursday 12-Oct Friday 13-Oct Saturday 14-Oct Sunday - Wikispaces check on each Sunday night by 9:00 pm
-- Clone your gene into accepting vector
ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc
15-Oct Monday 16-Oct Tuesday Virtual Screen Refresher - changed due date to tomorrow
17-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
Virtual Screen Refresher - due at midnight (Wed)
18-Oct Thursday 19-Oct Friday
LAB NOTEBOOK CHECK
20-Oct Saturday 21-Oct Sunday
- Wikispaces check on each Sunday night by 9:00 pm
Finish cloning
Check sequence, grow up large amount for Midi-prep
Transform into BL21(DE3) cells
Continue Virtual Screening of your target
-- the sooner this is done, the faster we can order compounds
ProtocolHomologyModelVDS_v3.doc
ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
Protocol_ICM_VDSv1_3.docx
15-Oct Monday 16-Oct Tuesday 17-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
18-Oct Thursday 19-Oct Friday
LAB NOTEBOOK CHECK
20-Oct Saturday 21-Oct Sunday - Wikispaces check on each Sunday night by 9:00 pm
-- Clone your gene into accepting vector
ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc
Begin Virtual Screening Protocols for your real target - not practice!
in GDOCS /Protocols/VirtualScreeningProtocols/
ProtocolHomologyModelVDS_v3.doc (if necessary)
ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
Protocol_ICM_VDSv1_3.docx
22-Oct Monday 23-Oct Tuesday
Research Report on Target Due @ midnight GuidelinesResearchReportonTarget_VDS_Fall12.doc 24-Oct Wednesday 25-Oct Thursday 26-Oct Friday 27-Oct Saturday 28-Oct Sunday
PyMol Image Contest - Wikispaces check on each Sunday night by 9:00 pm
Finish cloning
Check sequence, grow up large amount for Midi-prep
Transform into BL21(DE3) cells
Continue Virtual Screening of your target
-- the sooner this is done, the faster we can order compounds
ProtocolHomologyModelVDS_v3.doc
ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
Protocol_ICM_VDSv1_3.docx
22-Oct Monday 23-Oct Tuesday
Research Report on Target Due @ midnight GuidelinesResearchReportonTarget_VDS_Fall12.doc 24-Oct Wednesday 25-Oct Thursday 26-Oct Friday 27-Oct Saturday 28-Oct Sunday
PyMol Image Contest - Wikispaces check on each Sunday night by 9:00 pm
-- Clone your gene into accepting vector
ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc
Your protein should be setup for GOLD screening by this week
and CB306 library screened
29-OctMonday 30-OctTuesday 31-OctWednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion 1-Nov Thursday - Dr. B out of town
2-Nov Friday - Dr. B out of town 3-Nov Saturday - Dr. B out of town 4-Nov Sunday - Wikispaces check on each Sunday night by 9:00 pm
Your protein should be setup for GOLD screening by this week
and CB306 library screened and analyzed
and ChembridgeDiversity library should be started
29-OctMonday 30-OctTuesday 31-OctWednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion 1-Nov Thursday - Dr. B out of town 2-Nov Friday - Dr. B out of town 3-Nov Saturday - Dr. B out of town 4-Nov Sunday - Wikispaces check on each Sunday night by 9:00 pm
Finish cloning
OR
Start screening ChembridgeDiversity library
5-Nov Monday 6-Nov Tuesday Cloning Materials & Methods due
7-Nov Wednesday 8-Nov Thursday
Cloning Materials & Methods due
9-Nov Friday 10-NovSaturday 11-Nov Sunday - Wikispaces check on each Sunday night by 9:00 pm
Continue with cloning and/or protein expression
Analyze both CB306 andChembridgeDiversity library results
Create a TopLigands (protocol in GDocs) list and manually enter the Top 5 to the Google Docs spreadsheet
5-Nov Monday 6-Nov Tuesday Cloning Materials & Methods due
7-Nov Wednesday 8-Nov Thursday
Cloning Materials & Methods due
9-Nov Friday 10-NovSaturday 11-Nov Sunday - Wikispaces check on each Sunday night by 9:00 pm
Continue expressing, purifying your surrogate enzyme
Analyze your CB306 library screening results
Start CBKin-UT library. (4,000 ligands)
12-Nov Monday 13-Nov Tuesday
14-Nov Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
15-Nov Thursday 16-Nov Friday
LAB NOTEBOOK CHECk
17-Nov Saturday
18-Nov Sunday
Virtual M&M due - Sunday at 9 pm.
see VDSFall12_Guide_M&M_Virtual_VDS.docx in Google Docs
- Wikispaces check on each Sunday night by 9:00 pm
Analyze and post your library screening results to GDocs
OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds
12-Nov Monday 13-Nov Tuesday
14-Nov Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
15-Nov Thursday 16-Nov Friday
LAB NOTEBOOK CHECK
17-Nov Saturday 18-Nov Sunday
Virtual M&M due - Sunday at 9 pm.
see VDSFall12_Guide_M&M_Virtual_VDS.docx in Google Docs
- Wikispaces check on each Sunday night by 9:00 pm
Continue purifying and characterizing your surrogate enzyme
Analyze your CB306 library screening results
Start CBKin-UT library. (4,000 ligands)
19-Nov Monday
5-6 pm - Lab Group Meeting(in : RLM 12.166)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
20-Nov Tuesday 21-Nov Wednesday 22-Nov Thursday
23-Nov Friday 24-Nov Saturday 25-Nov Sunday - Wikispaces check on each Sunday night by 9:00 pm
Analyze and post your library screening results to GDocs
OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds
19-Nov Monday
5-6 pm - Lab Group Meeting(in : RLM 12.166)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
20-Nov Tuesday 21-Nov Wednesday 22-Nov Thursday
23-Nov Friday 24-Nov Saturday 25-Nov Sunday - Wikispaces check on each Sunday night by 9:00 pm
Enzyme assays with your surrogate enzyme: ProtocolEnzymeTest_Phosphatase_VDS_Fall12_varyEnzyme.xlsx
Start Inhibition assays. ProtocolEnzymeTest_Phosphatase_VDS_Fall12_Inhibition.xlsx
Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)
Analyze your CB306 library & CBKin-UT library screening results post your TopLigands to GDocs (Ignore ICM work)
26-Nov Monday
27-Nov Tuesday
Expression M&M due VDSFall12_Guide_M&M_ExpressionPurification_VDS.docxin Google Docs
28-Nov Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
no journal club
29-Nov Thursday
30-Nov Friday
1-Dec Saturday
2-Dec Sunday
- Wikispaces check on each Sunday night by 9:00 pm
continue with wet lab work
Start Inhibition assays (if you have protein). Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)
Analyze and post yourlibrary screening results to GDocs
(Ignore ICM work)
OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds
26-Nov Monday 27-Nov Tuesday
Expression M&M due VDSFall12_Guide_M&M_ExpressionPurification_VDS.docxin Google Docs
28-Nov Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
no journal club
29-Nov Thursday 30-Nov Friday 1-Dec Saturday 2-Dec Sunday - Wikispaces check on each Sunday night by 9:00 pm
FROM FALL 11 1st Week (8/31 – 9/2)
2nd Week (9/5 – 9/9)
3rd Week (9/12 – 9/16)
PyMol Refresher (see Announcement page for PyMol Help Session on Thursday 9/14)
Due next week for Returning Spring VDSers
Due week after next for New VDSers (Joshua, Hong, Marshall, Shreya, Indra)
Primary PCR with Oligo Mix ProtocolPCR_PrimerOverlapVDS_Fall11.docx
Secondary PCR w/ Tail primers same protocol
For Virtual Refresher:
Since the blades are full - you only need to have your first Run started by the end of this week. (by Friday 9/30)
VDSers that are returning from Spring:
Begin realVirtual Screening - prepare protein in GOLD and start jobs (cb306 should be done this week and the next one started)
Wikispaces check on each Friday Week 6 (10/3 – 10/7) Submit 2nd job of Virtual Screen Refresher Begin Virtual Screening on YOUR targetVirtual Screening
Continue cloning
complete both primer design exercises
complete 1st and 2nd Overlap PCR
Lab Notebook check this Friday (7:00 pm)
Wikispaces check on each Friday
Target Selection exercise ?
10/03/11 - Still need PyMol Refresher from: Michael E., Shutian J., Giancarlo M., Shreya N., Indra S. , Hong C.
Week 7 (10/10 – 10/14)
Journal Club 3
Research Report Due - Tues Oct. 11th - Guidelines in GDocs folder
Continue realVirtual Screening - prepare protein in GOLD and start jobs
Virtual Screening help session for setting up your protein (should have 1st library done this week)
Week 9 (10/24 – 10/28) VIRTUAL SCREENING - finish by this week - do Top Ligands Procotol to get final compounds for ordering
Journal Club 4
Express your enzyme Fri ( 10/28) Lab Notebook check this Friday(7:00 pm)
or Sat night if working on Sat.
Wikispaces check on each Friday
Week 10 (10/31 – 11/4) Tues Nov. 1st Thursday Nov 3rd at Midnight (Materials & Methods for Cloning due) FRI External Open House - Wednesday Nov. 2nd 1- 4 pm
Top Ligands Procotol to get final compounds for ordering
Express your enzyme
Purify and Characterize your protein
Wikispaces check on each Friday
Protein Expression Scheduling:
Here's the Sign Up Form on Google - new guys and returning Spring VDSers should fill this out by Monday night.
Week 11 (11/7 – 11/11)
Journal Club 5
Tues Nov. 8th at Midnight (Materials & Methods for Virtual Screening due) - see Tips & Hints page
Enzyme Assays
Wikispaces check on each Friday Week 12 (11/14 – 11/18) Tues Nov. 15th at Midnight (Materials & Methods for Expression, Purification, and Characterization due)
Purify and Characterize your protein - NOTE: this is a long and arduous process. Don't put it off.
Enzyme Assays
Inhibition Assays Fri ( 11/18) Lab Notebook check this Friday(7:00 pm)
or Sat night if working on Sat.
Wikispaces check on each Friday
Protein Protocols to be completed - also see instructional videos on GDocs
ProtocolProteinExpression_VDS_Fall11_ver2.doc
ProtocolProteinPurificationVDS_Fall11.doc ProtocolHomemadeSDSPageGelSolutionsVDS_Fall11.docx - Skip this one (the Mentors will make gels for you)
ProtocolProteinCharacterizationVDS_Fall11.doc
ProtocolFPLC_GelFiltration_VDS_Fall11V_v2.docx
ProtocolLabEnzymeTest_Phosphatase_VDS_Fall11.xlsx
Then on to Inhibition Assays once compounds arrive
Week 13 (11/21 – 11/25): Thanksgiving
Journal Club 6
Inhibition Assays - on 2 compounds
Wikispaces check on each Friday
Week 14 (11/28 – 12/2)
Inhibition Assays - on 2 compounds
Tues Nov. 29th - FINAL PRESENTATIONS of Enzyme Inhibition Graphs- everyone
make a one slide PowerPoint and upload to the GroupMeetingSlides/FInalSlides_StudentsFall11 folder on GDocs
save file with your name and date in the file name
Thurs (12/1) - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time) Fri (12/2) - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
Sat ( 12/3) Final Report due (5:00 pm ) Final Lab Notebook check (7:00 pm)
Final Wikispaces check
TIMELINE FOR RESEARCH
Schedule of things we will do over the semesterResearcher's Names:
- Summer Veterans: Aldo, Andrew, Michael, Daniel, Janice, Max, Urvashi, Alex, Kaarthik, Aakash,
- Sidestreamers: Akhilesh, Rishi, Paul, Priya, Vanna, Keyur, Ben, Jennifer
- Springers: Shane, Suman, Stephanie, Divya, Brandon, Ivy, Sajan, Tom, Mihir, Rufei, Ling
NOTE - see middle of page for previous weeks' schedules and things to catch up on.Definitions: 'cubby' = VDS cabinet in back of lab where all of our reagents are; 'pigeon hole' = the shelf for your lab notebook over by the window
This Week
This Week
Enzyme assays with your surrogate enzyme:
ProtocolEnzymeTest_Phosphatase_VDS_Fall12_varyEnzyme.xlsx
Start Inhibition assays.
ProtocolEnzymeTest_Phosphatase_VDS_Fall12_Inhibition.xlsx
Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)
Finish Virtual Screening
cb306 and CBkinUT
3-Dec Monday
4-Dec Tuesday
5-Dec Wednesday
LAST VDS CLASS
Class Picture!
In class on Wednesday (12/5) - around 75% of the way through class ~ 2:45
VDSers - don't forget to fill out the CIS forms online. We won't do a paper version this semester.
CH 369K (52275) https://utdirect.utexas.edu/ctl/ecis/
6-Dec Thursday
Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
7-Dec Friday
Lab Cleanup
8-Dec Saturday
Final Lab Report Due
Final LAB NOTEBOOK CHECK
9-Dec Sunday
continue with wet lab work
Start Inhibition assays. Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)
Analyze and post your library screening results to GDocs
3-Dec Monday
4-Dec Tuesday
5-Dec Wednesday
LAST VDS CLASS
Class Picture!
In class on Wednesday (12/5) - around 75% of the way through class ~ 2:45
VDSers - don't forget to fill out the CIS forms online. We won't do a paper version this semester.
CH 369K (52275) https://utdirect.utexas.edu/ctl/ecis/
6-Dec Thursday
Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
7-Dec Friday
Lab Cleanup
8-Dec Saturday
Final Lab Report Due
Final LAB NOTEBOOK CHECK
9-Dec Sunday
Next Week
Next Week
Protein Protocols to be completed - also see instructional videos on GDocs
ProtocolProteinExpression_VDS_Fall12.docProtocolProteinPurificationVDS_Fall12.doc
ProtocolHomemadeSDSPageGelSolutionsVDS_Fall12.docx - Skip this one (the Mentors will make gels for you)
ProtocolProteinCharacterizationVDS_Fall12.doc
ProtocolFPLC_GelFiltration_VDS_Fall12.docx
ProtocolLabEnzymeTest_Phosphatase_VDS_Fall12.xlsx
Enzyme Assays on target
Inhibition Assays on target
Optional: VINA tutorial
BASH or Perl script
11-DecTuesday
12-DecWednesday
13-DecThursday
14-DecFriday
15-DecSaturday
16-DecSunday
11-DecTuesday
12-DecWednesday
13-DecThursday
14-DecFriday
15-DecSaturday
16-DecSunday
PAST DATE
Target Discovery
Target Discovery - order primers
DATE-SPECIFIC ITEMS
27-Aug Monday
28-Aug Tuesday
29-Aug Wednesday
2 - 3pm - Lab Group Meeting - RLM 11.176
Create a GDocs folder in /StudentFolders - FirstnameLastInitial (e.g. WilliamB)
Create a Wikispaces page under Research Pages
3:30 - 6pm - Target Discovery Session in WEL 2.114
--Pick new target
30-Aug Thursday
Target Discovery Session (1-5 pm in WEL 2.114)
--Pick new target
31-Aug Friday
ORDER Primers for you target
PRIMER ORDERING SESSION: 1 - 4:30 in WEL 2.114 - Comp Lab
Spreadsheet for ordering primers is at:
Google Docs/VDS/Misc/Primers/PrimerPlateOrderTemplate_GDocs_AugFall_2012
Wikispaces check on each Friday
Your WikiPage should have: been created by now, brief detail of what you have done these last 3 days
PAPER COPY – Print out of TxClass Safety Training
- (can put in Safety section of VDS sign-in binder in lab)
submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev)
-- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc
1-Sep Saturday
2-Sep Sunday
Download & print needed protocols from GDocs
-- under /Protocols/Cloning/FirstProtocols
Submit to DNA Sequencing
-- in 2 days retrieve and save results to your GDocs folder
RE Digest
-- save results to your GDocs folder
-- post image commentary to your Wikispace page
Analyze DNA sequence exercise
Virtual Screening Refresher
Transform positive clone with your gene into BL21(De3) cells - begin expression
PyMol Refresher - Due by ??
Science Works assignment due ??
27-Aug Monday
28-Aug Tuesday
29-Aug Wednesday
2 - 3pm - Lab Group Meeting/Journal Club (in ???? classroom)
30-Aug Thursday
31-Aug Friday
PyMol Refresher - due next Wed
Wikispaces check on each Friday
1-Sep Saturday
2-Sep Sunday
-- in 2 days retrieve and save results to your GDocs folder
RE Digest
-- save results to your GDocs folder
-- post image commentary to your Wikispace page
3-Sep Monday
12 - 4 pm Target Discovery & Primer Design & Primer ordering
Spreadsheet for ordering primers is at:
Google Docs/VDS/Misc/Primers/PrimerPlateOrderTemplate_GDocs_AugFall_2012
4-Sep Tuesday
If your primers have been uploaded:
ProtocolPrimerDilutionVDS_Fall12.docx (use pLIC for or pLIC rev)
-- submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev)
---- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc
Target Discovery
PAPER COPY – Print out of TxClass Safety Training
- (can put in Safety section of VDS sign-in binder in lab)
5-Sep Wednesday
2 - 3pm - Lab Group Meeting (in RLM 11.176 classroom)
ProtocolPrimerDilutionVDS_Fall12.docx (use pLIC for or pLIC rev) (~1.5 hrs)
-- submit pNIC-Bsa4 to sequencing (pLICfor & pLICrev)
---- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall12.doc
Transformation of pNIC-Bsa4 in Dh5alpha (~2-2.5 hrs)
6-Sep Thursday
Retrieve results on line from DNA Sequencing core website for your results from:
-- "Submit to DNA Sequencing"
- save results to your GDocs folder
RE digest & Agarose Gel - of pGBR22
--- ProtocolRestrictionEnzymeDigestVDS.doc (~4hrs with break)
--- ProtocolNanoDropVDS.doc (~2hrs)
Transformation of pNIC-Bsa4 in Dh5alpha
7-Sep Friday
Springers - Finish up your Target page that you created in Target Discovery Protocol, even if it was not one that was chosen. This will be for a grade.
3:30 - 6:30 Analyze DNA sequence exercise (in WELCH computer lab)
-- save the assignment as WORD doc to your GDocs folder
Wikispaces check on each Friday
Your WikiPage should have
8-Sep Saturday
9-Sep Sunday
- Help Sessions: PyMol and Virtual Screen Refresher Welch Computer Lab
4-Sep Tuesday5-Sep Wednesday
2 - 3pm - Lab Group Meeting (in RLM 11.176 classroom)
PyMol Refresher - due today
6-Sep Thursday
7-Sep Friday
New Overlap PCR protocol posted to GDocs that uses new Q5 polymerase from NEB -- courtesy of Kaarthik
---ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall12.docx
You can use either Q5 or KOD polymerase. But we are out of KOD right now!
8-Sep Saturday
9-Sep Sunday
--- ProtocolRestrictionEnzymeDigestVDS.doc (~4hrs with break)
--- ProtocolNanoDropVDS.doc (~2hrs)
2. Retrieve results on line from DNA Sequencing core website for your results from:
-- "Submit to DNA Sequencing"
- save results to your GDocs folder
PAPER COPY – Print out of TxClass Safety Training
- (can put in Safety section of VDS sign-in binder in lab)
3. Grow up pNIC_bsa4 in DH5alpha o/n in 1x160ml - store pellets
4. Midi prep pNIC-Bsa4 (later in week - Th or Fri in groups)
5. Practice PCR #1: ProtocolPCRVDS.xls with TAQ poly
10-SepMonday
11-SepTuesday
12-SepWednesday
2 - 3pm - Lab Group Meeting(in NEW classroom: RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
13-SepThursday
14-SepFriday --FRI Picnic (Mentors & Dr. B)
Lab Notebook Check this Friday - leave your notebook in your 'pigeon hole' in lab by 7:00 pm
15-SepSaturday
16-SepSunday - Wikispaces check on each Sunday night by 9:00 pm
New Overlap PCR protocol posted to GDocs that uses new Q5 polymerase from NEB -- courtesy of Kaarthik
---ProtocolPCR_PrimerOverlapWithQ5Polymerase_VDS_Fall12.docx
Virtual Screen Refresher - due next week (Friday Sept 22nd)
10-SepMonday
11-SepTuesday
12-SepWednesday
2 - 3pm - Lab Group Meeting(in NEW classroom: RLM 10.176)
--------- includes JOURNAL CLUB*
13-SepThursday
14-SepFriday
--5-7pm FRI Picnic (Mentors & Dr. B)
Lab Notebook Check this Friday - leave your notebook in your 'pigeon hole' in lab by 7:00 pm
15-SepSaturday
16-SepSunday - Wikispaces check on each Sunday night by 9:00 pm
Should have already completed: RE digest, Nanodrop, Submit to DNA, Analyze DNA, Transformation, etc.
(NOTE: be sure to post your Nanodrop concentrations of pNIC-Bsa4 from MidiPrep on the Google Docs spreadsheet
- in /Misc/PlasmidConcentrations. ONLY a few of you have uploaded yours.
17-SepMonday
18-SepTuesday
19-SepWednesday -
2 - 3pm - Lab Group Meeting(in NEW classroom: RLM 10.176)
20-SepThursday
21-SepFriday ? FRI Picnic (Mentors & Dr. B)??
22-SepSaturday
23-SepSunday
- Wikispaces check on each Sunday night by 9:00 pm
Continue cloning
Virtual Screen Refresher - due (Friday Sept 22nd)
17-SepMonday
18-SepTuesday
19-SepWednesday
2 - 3pm - Lab Group Meeting(in NEW classroom: RLM 10.176)
20-SepThursday
21-SepFriday ? FRI Picnic (Mentors & Dr. B)??
22-SepSaturday
23-SepSunday
- Wikispaces check on each Sunday night by 9:00 pm
- in /Misc/PlasmidConcentrations. ONLY a few of you have uploaded yours.
Design Tail Primers ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall12.doc -
ProtocolPCR_PrimerOverlapVDS_fall12.docx
- 1st step is to Make Oligo Mix (takes an hour or two)
24-SepMonday
25-SepTuesday
26-SepWednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
27-SepThursday
28-SepFriday
29-SepSaturday
PyMol refresher due date changed to this Saturday Sept 29th
30-SepSunday
- Wikispaces check on each Sunday night by 9:00 pm
-- PyMol refresher due date changed again to this Sunday Sept 30th - i would rather you focus on your
---- ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall12.doc
25-SepTuesday
26-SepWednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
27-SepThursday
28-SepFriday
29-SepSaturday
30-SepSunday
- Wikispaces check on each Sunday night by 9:00 pm
-- 1st step: Make Oligo Mix
-- 2nd step: Primary PCR
-- 3rd step: Secondary PCR - need your custom 'tail' primers for this
-- RE digest of pNIC-Bsa4 (save for yourself and use for cloning) - NOTE: different than last RE digest
------ takes 4 hrs (3 hours of incubation in 37degC water bath - you can leave during this time)
-- Clone your gene into accepting vector
---------ProtocolpNIC-Bsa4_cloningVDS_Fall12.doc
1-Oct Monday
Design Tail Primers ProtocolPCR_PrimerDesign_for_pNIC-Bsa4CloningFall12.doc -
2-Oct Tuesday
3-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
4-Oct Thursday
5-Oct Friday
6-Oct Saturday
7-Oct Sunday
- Wikispaces check on each Sunday night by 9:00 pm
(NOTE: be sure to post your Nanodrop concentrations of pNIC-Bsa4 from MidiPrep on the Google Docs spreadsheet
- in /Misc/PlasmidConcentrations. ONLY a few of you have uploaded yours.
Should be getting closer to finishing cloning
1-Oct Monday
2-Oct Tuesday
3-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
4-Oct Thursday
5-Oct Friday
6-Oct Saturday
7-Oct Sunday
- Wikispaces check on each Sunday night by 9:00 pm
-- 2nd step: Primary PCR
-- 3rd step: Secondary PCR - need your custom 'tail' primers for this
-- RE digest of pNIC-Bsa4 (save for yourself and use for cloning) - NOTE: different than last RE digest
------ takes 4 hrs (3 hours of incubation in 37degC water bath - you can leave during this time)
-- Clone your gene into accepting vector
8-Oct Monday
9-Oct Tuesday
10-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
11-Oct Thursday
12-Oct Friday
13-Oct Saturday
14-Oct Sunday
- Wikispaces check on each Sunday night by 9:00 pm
Virtual Screening Protocols are posted (these are for your real target - not practice)
in GDOCS /Protocols/VirtualScreeningProtocols/
8-Oct Monday
9-Oct Tuesday
10-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
11-Oct Thursday
12-Oct Friday
13-Oct Saturday
14-Oct Sunday
- Wikispaces check on each Sunday night by 9:00 pm
15-Oct Monday
16-Oct Tuesday
Virtual Screen Refresher - changed due date to tomorrow
17-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
Virtual Screen Refresher - due at midnight (Wed)
18-Oct Thursday
19-Oct Friday
LAB NOTEBOOK CHECK
20-Oct Saturday
21-Oct Sunday
- Wikispaces check on each Sunday night by 9:00 pm
Check sequence, grow up large amount for Midi-prep
Transform into BL21(DE3) cells
Continue Virtual Screening of your target
-- the sooner this is done, the faster we can order compounds
15-Oct Monday
16-Oct Tuesday
17-Oct Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
18-Oct Thursday
19-Oct Friday
LAB NOTEBOOK CHECK
20-Oct Saturday
21-Oct Sunday
- Wikispaces check on each Sunday night by 9:00 pm
Begin Virtual Screening Protocols for your real target - not practice!
in GDOCS /Protocols/VirtualScreeningProtocols/
22-Oct Monday
23-Oct Tuesday
Research Report on Target Due @ midnight
GuidelinesResearchReportonTarget_VDS_Fall12.doc
24-Oct Wednesday
25-Oct Thursday
26-Oct Friday
27-Oct Saturday
28-Oct Sunday
PyMol Image Contest
- Wikispaces check on each Sunday night by 9:00 pm
Check sequence, grow up large amount for Midi-prep
Transform into BL21(DE3) cells
Continue Virtual Screening of your target
-- the sooner this is done, the faster we can order compounds
- ProtocolHomologyModelVDS_v3.doc
- ProtocolVirtualScreenYOURTarget_VDS_Fall12.doc
- ProtocolVirtualScreenTopLigands_VDS_Fall12.doc
- Protocol_ICM_VDSv1_3.docx
22-Oct Monday23-Oct Tuesday
Research Report on Target Due @ midnight
GuidelinesResearchReportonTarget_VDS_Fall12.doc
24-Oct Wednesday
25-Oct Thursday
26-Oct Friday
27-Oct Saturday
28-Oct Sunday
PyMol Image Contest
- Wikispaces check on each Sunday night by 9:00 pm
Your protein should be setup for GOLD screening by this week
and CB306 library screened
29-OctMonday
30-OctTuesday
31-OctWednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
1-Nov Thursday - Dr. B out of town
2-Nov Friday - Dr. B out of town
3-Nov Saturday - Dr. B out of town
4-Nov Sunday
- Wikispaces check on each Sunday night by 9:00 pm
and CB306 library screened and analyzed
and ChembridgeDiversity library should be started
29-OctMonday
30-OctTuesday
31-OctWednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
1-Nov Thursday - Dr. B out of town
2-Nov Friday - Dr. B out of town
3-Nov Saturday - Dr. B out of town
4-Nov Sunday
- Wikispaces check on each Sunday night by 9:00 pm
OR
Start screening ChembridgeDiversity library
5-Nov Monday
6-Nov Tuesday
Cloning Materials & Methods due
7-Nov Wednesday
8-Nov Thursday
Cloning Materials & Methods due
9-Nov Friday
10-NovSaturday
11-Nov Sunday
- Wikispaces check on each Sunday night by 9:00 pm
Analyze both CB306 and ChembridgeDiversity library results
Create a TopLigands (protocol in GDocs) list and manually enter the Top 5 to the Google Docs spreadsheet
5-Nov Monday
6-Nov Tuesday
Cloning Materials & Methods due
7-Nov Wednesday
8-Nov Thursday
Cloning Materials & Methods due
9-Nov Friday
10-NovSaturday
11-Nov Sunday
- Wikispaces check on each Sunday night by 9:00 pm
Analyze your CB306 library screening results
Start CBKin-UT library. (4,000 ligands)
12-Nov Monday
13-Nov Tuesday
14-Nov Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
15-Nov Thursday
16-Nov Friday
LAB NOTEBOOK CHECk
17-Nov Saturday
18-Nov Sunday
Virtual M&M due - Sunday at 9 pm.
see VDSFall12_Guide_M&M_Virtual_VDS.docx in Google Docs
- Wikispaces check on each Sunday night by 9:00 pm
OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds
12-Nov Monday
13-Nov Tuesday
14-Nov Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
15-Nov Thursday
16-Nov Friday
LAB NOTEBOOK CHECK
17-Nov Saturday
18-Nov Sunday
Virtual M&M due - Sunday at 9 pm.
see VDSFall12_Guide_M&M_Virtual_VDS.docx in Google Docs
- Wikispaces check on each Sunday night by 9:00 pm
Analyze your CB306 library screening results
Start CBKin-UT library. (4,000 ligands)
19-Nov Monday
5-6 pm - Lab Group Meeting(in : RLM 12.166)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
20-Nov Tuesday
21-Nov Wednesday
22-Nov Thursday
23-Nov Friday
24-Nov Saturday
25-Nov Sunday
- Wikispaces check on each Sunday night by 9:00 pm
OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds
19-Nov Monday
5-6 pm - Lab Group Meeting(in : RLM 12.166)
--------- includes JOURNAL CLUB*
-- read the article at least 2 times and answer questions to turn in at start of class
-- bring a PAPER copy of article with you for Discussion
20-Nov Tuesday
21-Nov Wednesday
22-Nov Thursday
23-Nov Friday
24-Nov Saturday
25-Nov Sunday
- Wikispaces check on each Sunday night by 9:00 pm
ProtocolEnzymeTest_Phosphatase_VDS_Fall12_varyEnzyme.xlsx
Start Inhibition assays.
ProtocolEnzymeTest_Phosphatase_VDS_Fall12_Inhibition.xlsx
Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)
Analyze your CB306 library & CBKin-UT library screening results
post your TopLigands to GDocs (Ignore ICM work)
26-Nov Monday
27-Nov Tuesday
Expression M&M due
VDSFall12_Guide_M&M_ExpressionPurification_VDS.docx in Google Docs
28-Nov Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
no journal club
29-Nov Thursday
30-Nov Friday
1-Dec Saturday
2-Dec Sunday
- Wikispaces check on each Sunday night by 9:00 pm
Start Inhibition assays (if you have protein). Use your surrogate enzyme with ONE of the In House Compounds that we have in the lab. These compounds are diluted in DMSO to 5 mM (don't use the 50 mM Stocks)
Analyze and post yourlibrary screening results to GDocs
(Ignore ICM work)
OPTIONAL: Screen HF9 plates 5-9 library and InHouseCompounds
26-Nov Monday
27-Nov Tuesday
Expression M&M due
VDSFall12_Guide_M&M_ExpressionPurification_VDS.docx in Google Docs
28-Nov Wednesday
2 - 3pm - Lab Group Meeting(in : RLM 10.176)
no journal club
29-Nov Thursday
30-Nov Friday
1-Dec Saturday
2-Dec Sunday
- Wikispaces check on each Sunday night by 9:00 pm
FROM FALL 11
1st Week (8/31 – 9/2)
2nd Week (9/5 – 9/9)
3rd Week (9/12 – 9/16)
PyMol Refresher (see Announcement page for PyMol Help Session on Thursday 9/14)
Once you have successfully completed first PCR,
Science Works assignment due Friday Sept 16th - see announcement page
Lab Notebook Check this Friday - leave your notebook in 'Drug Screening Notebooks' drawer in lab by 7:00 pm
- all protocols (PCR , RE Digest, analyze DNA, submit DNA)
- all gel images
- Analyze DNA Sequence exercise work
- Protocol, Order form and Results from ProtocolDNASequencingFacilityVDS_Fall11.doc
Wikispaces check on each Friday4th Week (9/19 – 9/23)
PyMol Refresher
Virtual Screen Refresher - due next week (Tues 9/27)
Wikispaces check on each Friday
Week 5 (9/26 – 9/30)
begin cloning
For Virtual Refresher:
Since the blades are full - you only need to have your first Run started by the end of this week. (by Friday 9/30)
VDSers that are returning from Spring:
Wikispaces check on each Friday
Week 6 (10/3 – 10/7)
Submit 2nd job of Virtual Screen Refresher
Begin Virtual Screening on YOUR target Virtual Screening
Continue cloning
Lab Notebook check this Friday (7:00 pm)
Wikispaces check on each Friday
Target Selection exercise ?
10/03/11 - Still need PyMol Refresher from: Michael E., Shutian J., Giancarlo M., Shreya N., Indra S. , Hong C.
Week 7 (10/10 – 10/14)
Journal Club 3
Research Report Due - Tues Oct. 11th - Guidelines in GDocs folder
Continue real Virtual Screening - prepare protein in GOLD and start jobs
PyMol Image contest Due Friday at Midnight
Wikispaces check on each Friday
Week 8 (10/17 – 10/21)
VIRTUAL SCREENING - should have 3 libraries completed.
Perform cloning protocol on your target:
- ProtocolpNIC-Bsa4_cloningVDS_Fall11.doc
verify positive clones with- ProtocolDNASequencingFacilitypNIC-Bsa4_VDS_Fall11.doc
Wikispaces check on each FridayWeek 9 (10/24 – 10/28)
VIRTUAL SCREENING - finish by this week - do Top Ligands Procotol to get final compounds for ordering
Journal Club 4
Express your enzyme
Fri ( 10/28) Lab Notebook check this Friday(7:00 pm)
or Sat night if working on Sat.
Wikispaces check on each Friday
Week 10 (10/31 – 11/4)
Tues Nov. 1st Thursday Nov 3rd at Midnight (Materials & Methods for Cloning due)
FRI External Open House - Wednesday Nov. 2nd 1- 4 pm
Top Ligands Procotol to get final compounds for ordering
Express your enzyme
Purify and Characterize your protein
Wikispaces check on each Friday
Protein Expression Scheduling:
Here's the Sign Up Form on Google - new guys and returning Spring VDSers should fill this out by Monday night.Week 11 (11/7 – 11/11)
Journal Club 5
Tues Nov. 8th at Midnight (Materials & Methods for Virtual Screening due) - see Tips & Hints page
Enzyme Assays
Wikispaces check on each Friday
Week 12 (11/14 – 11/18)
Tues Nov. 15th at Midnight (Materials & Methods for Expression, Purification, and Characterization due)
Purify and Characterize your protein - NOTE: this is a long and arduous process. Don't put it off.
Enzyme Assays
Inhibition Assays
Fri ( 11/18) Lab Notebook check this Friday(7:00 pm)
or Sat night if working on Sat.
Wikispaces check on each Friday
Protein Protocols to be completed - also see instructional videos on GDocs
ProtocolProteinExpression_VDS_Fall11_ver2.docProtocolProteinPurificationVDS_Fall11.doc
ProtocolHomemadeSDSPageGelSolutionsVDS_Fall11.docx - Skip this one (the Mentors will make gels for you)
ProtocolProteinCharacterizationVDS_Fall11.doc
ProtocolFPLC_GelFiltration_VDS_Fall11V_v2.docx
ProtocolLabEnzymeTest_Phosphatase_VDS_Fall11.xlsx
Then on to Inhibition Assays once compounds arrive
Week 13 (11/21 – 11/25): Thanksgiving
Journal Club 6
Inhibition Assays - on 2 compounds
Wikispaces check on each Friday
Week 14 (11/28 – 12/2)
Inhibition Assays - on 2 compounds
Tues Nov. 29th - FINAL PRESENTATIONS of Enzyme Inhibition Graphs- everyone
make a one slide PowerPoint and upload to the GroupMeetingSlides/FInalSlides_StudentsFall11 folder on GDocs
save file with your name and date in the file name
Thurs (12/1) - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
Fri (12/2) - Lab Cleanup (Required) - each students spends 1 hr cleaning in lab (counts as 1 hour of lab time)
Sat ( 12/3)
Final Report due (5:00 pm )
Final Lab Notebook check (7:00 pm)
Final Wikispaces check